{"id":"W4392810639","doi":"10.1101/2024.03.13.584690","title":"Mutability and hypermutation antagonize immunoglobulin codon optimality","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; Centers for Disease Control and Prevention; Bill and Melinda Gates Foundation","keywords":"Somatic hypermutation; Biology; Germline; Genetics; Affinity maturation; Cytidine deaminase; Codon usage bias; Gene; Paratope; Stop codon; Antibody; Monoclonal antibody; Genome; B cell","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000314292,0.0002328144,0.0002148119,0.000341868,0.0001302089,0.0005786755,0.0002006172,0.000224035,0.0008432315],"category_scores_gemma":[0.0005810407,0.0001532678,0.0001939607,0.0001679074,0.0004096813,0.0002606863,0.0004329754,0.000416779,0.0001519426],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003954804,"about_ca_system_score_gemma":0.0001889669,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002679141,"about_ca_topic_score_gemma":0.0005152414,"domain_scores_codex":[0.999652,0.00006881227,0.00002539073,0.00006081483,0.0001115773,0.00008141347],"domain_scores_gemma":[0.99941,0.0001529338,0.0002486022,0.00005414206,0.00006070341,0.00007351006],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00007082427,0.00001069564,0.004277627,0.00002017108,0.00001330805,0.00003446022,0.00001171257,0.000261049,0.9931198,0.0003667646,0.00001405886,0.001799567],"study_design_scores_gemma":[0.0000166712,0.0005618994,0.1185346,0.00001634099,0.00005498236,0.0007278394,0.000130917,0.009817173,0.8668365,0.0009935329,0.002288243,0.00002120461],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976099,0.0002229183,0.001404925,0.00002363741,0.000002625157,0.000004536998,0.00002643498,0.00001930155,0.0006857409],"genre_scores_gemma":[0.9991822,0.0000571703,0.0005059871,0.00002048516,0.000003397188,0.000002646305,0.00003312559,0.000008361023,0.0001866629],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008432315,"threshold_uncertainty_score":0.002869427,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01203872058446497,"score_gpt":0.2206309531959655,"score_spread":0.2085922326115005,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}